October 13, 2020

Today’s mid-week digest is about – meta analysis of metabolic benefits of probiotics, probiotics and synbiotics, microbiome association with narcolepsy type 1, design of microbial consortium for reduced C. difficle colonization, new sequencing technique for pathogen identification in cerebrospinal fluid and many more… Happy reading!

Human microbiome

The effect of probiotics, prebiotics or synbiotics on metabolic outcomes in individuals with diabetes: a systematic review and meta-analysis – Patricia M. Bock – Diabetologia

Effect of a Nonoptimal Cervicovaginal Microbiota and Psychosocial Stress on Recurrent Spontaneous Preterm Birth – Kristin D. Gerson – American Journal of Perinatology

Targeting the microbiome-gut-brain axis for improving cognition in schizophrenia and major mood disorders: A narrative review – Miquel Bioque – Progress in Neuro-Psychopharmacology and Biological Psychiatry

Inflammatory Bowel Disease Environmental Risk Factors: Diet and Gut Microbiota – Sarah Altajar – Current Gastroenterology Reports

Co‐ and polymicrobial infections in the gut mucosa: the host‐microbiota‐pathogen perspective – Teresa Frisan – Cellular Microbiology

Gut microbiota composition is associated with narcolepsy type 1 – Alexandre Lecomte – Neurology

A parental transcriptional response to microsporidia infection induces inherited immunity in offspring – Alexandra R. Willis – BioRxiv

Melamine contamination and associated health risks: Gut microbiota does make a difference – Meenakshi Rajpoot – Biotechnology and Applied Biochemistry

Animal microbiome

Rational design of a microbial consortium of mucosal sugar utilizers reduces Clostridiodes difficile colonization – Fátima C. Pereira – Nature Communications

Effects of seasonality and previous logging on faecal helminth-microbiota associations in wild lemurs – I. I. de Winter – Scientific Reports

Bacterial community analysis on the different mucosal immune inductive sites of gastrointestinal tract in Bactrian camels – Wang-Dong Zhang – PlosOne

Sows affect their piglets’ faecal microbiota until fattening but not their Salmonella enterica shedding status – Guillaume Larivière‐Gauthier – Letters in Applied Microbiology

Plant, root and soil microbiome

Comparison of soil microbial community between reseeding grassland and natural grassland in Songnen Meadow – Ruifen Zhu – Scientific Reports

Evidence for signatures of ancient microbial life in paleosols – Katharina Frindte – Scientific Reports

Techniques

Pathogen identification in culture-negative cerebrospinal fluid specimens of patients with purulent meningitis using next-generation sequencing technology – Xin Men – International Journal of Clinical Experimental Pathology

October 2, 2020

Today’s exciting updates – FMT method to restore normal microbial development in caesarean-born infants, mechanism unveiled how dietary tryptophan improves alcohol induced liver injury, advance in droplet based microfluidics to study host-microbiome interactions, prebiotics encapsulation of probiotic to suppress colon cancer and new hope to curb plastic waste by discovery of plastic-eating enzyme cocktail. Happy weekend, stay safe!

General microbiome

Eligible blood donors’ decisions about donating stool for fecal microbiota transplantation: Does ambivalence play a role? – Melissa K. Hyde – Transfusion

Microbiota-Dependent Effects of IL-22 – Morsal Sabihi – Cells

Human microbiome

Maternal Fecal Microbiota Transplantation in Cesarean-Born Infants Rapidly Restores Normal Gut Microbial Development: A Proof-of-Concept Study – Katri Korpela – Cell

Comparative analysis of the tonsillar microbiota in IgA nephropathy and other glomerular diseases – Ji In Park – Scientific Reports

Dysbiosis in the oral microbiomes of anti-CCP positive individuals at risk of developing rheumatoid arthritis – Zijian Cheng – Annals of the Rheumatic Diseases

Animal microbiome

Microbiota tryptophan metabolism induces aryl hydrocarbon receptor activation and improves alcohol-induced liver injury – Laura Wrzosek – Gut

Faecal microbiota transplant from aged donor mice affects spatial learning and memory via modulating hippocampal synaptic plasticity- and neurotransmission-related proteins in young recipients – Alfonsina D’Amato – Microbiome

Competitive reduction of poultry-borne enteric bacterial pathogens in chicken gut with bioactive Lactobacillus casei – Zajeba Tabashsum – Scientific Reports

Offspring susceptibility to metabolic alterations due to maternal high-fat diet and the impact of inhaled ozone used as a stressor – Samantha J. Snow – Scientific Reports

Beneficial effects of mung bean seed coat on the prevention of high-fat diet-induced obesity and the modulation of gut microbiota in mice – Dianzhi Hou – European Journal of Nutrition

Prebiotics‐Encapsulated Probiotic Spores Regulate Gut Microbiota and Suppress Colon Cancer – Di‐Wei Zheng – Advanced Materials

Multi-Omic Analysis Reveals Different Effects of Sulforaphane on the Microbiome and Metabolome in Old Compared to Young Mice – Se-Ran Jun – Microorganisms

Plant microbiome

Protists as catalyzers of microbial litter breakdown and carbon cycling at different temperature regimes – Stefan Geisen – Isme Journal

Techniques

Investigating host-microbiome interactions by droplet based microfluidics – Alexandra S. Tauzin – Microbiome

Non-specific amplification of human DNA is a major challenge for 16S rRNA gene sequence analysis – Sidney P. Walker – Scientific Reports

Non-microbiology picks

Plastic-eating enzyme ‘cocktail’ heralds new hope for plastic waste – Science Daily

September 1, 2020

Today’s post consists of review article on short chain fatty acids, research articles on efficacy of fecal microbiota transplant in patients with C. difficle infection and comorbities, identification of potential microbial biomarkers for preterm birth and a new technique to perform ultrafast microbial community analysis. Happy reading!

General microbiome

A systematic review of the effect of dietary pulses on microbial populations inhabiting the human gut – C.P.F. Marinangeli – Beneficial Microbes

Short chain fatty acids in human gut and metabolic health – E E Blaak – Beneficial Microbes

Human microbiome

The gut microbiome–derived metabolite trimethylamine N-oxide modulates neuroinflammation and cognitive function with aging – Vienna E. Brunt – Geroscience

Impact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial – Suryang Kwak – Microbiome

Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection in Patients With Multiple Comorbidities: Long-Term Safety and Efficacy Results From a Tertiary Care Community Hospital – Charumathi Raghu Subramanian – Gastroenterology Research

Gut commensal microbiota and decreased risk for Enterobacteriaceae bacteriuria and urinary tract infection – Matthew Magruder – Gut Microbes

Leveraging sequence‐based faecal microbial community survey data to identify alterations in gut microbiota among patients with Parkinson’s disease – Tianyi Ji – European Journal of Neuroscience

Plasma enterobacterial ClpB levels and ClpB- and α-MSH–reactive immunoglobulins in lung cancer patients with and without anorexia – Alessio Molfino – Nutrition

Identification of Potential Biomarkers in the Cervicovaginal Fluid by Metabolic Profiling for Preterm Birth – AbuZar Ansari – Metabolites

Plant microbiome

Suppression of rice planthopper populations without affecting the rice microbiota by the entomopathogenic fungus Metarhizium anisopliae – Yifan Peng – Applied and Environmental Microbiology

Cold Plasma Treatment of Sunflower Seeds Modulates Plant-Associated Microbiome and Stimulates Root and Lateral Organ Growth – Inga Tamošiūnė – Frontiers in Plant Science

Water microbiome

Bradymonabacteria, a novel bacterial predator group with versatile survival strategies in saline environments – Da-Shuai Mu – Microbiome

Techniques

Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2 – Jennifer Lu – Microbiome

Non-microbiology picks

Clinical characteristics of children and young people hospitalised with covid-19 in the United Kingdom: prospective multicentre observational cohort study – Olivia V Swann – BMJ

July 10, 2020

Today’s digest contains many exciting articles – gut microbiome in precision medicine for cancer, important review on patent protection in microbiome therapeutics, role of the gut microbiota in sympathetic neurons, interaction of pacemaker neurons with the gut microbiota, gut dysbiosis in lupus and many more….Enjoy reading and happy weekend!

General microbiome

Gut microbiome, big data and machine learning to promote precision medicine for cancer – Giovanni Cammarota – Nature Reviews Gastroenterology and Hepatology

Co-evolution and Co-speciation of Host-Gut Bacteria Systems – Mathieu Groussin – Cell Host and Microbe

Microbiome therapeutics and patent protection – Mark J. FitzGerald – Nature Biotechnology

Human microbiome

Fecal Microbiota Transplantation is Safe and Effective in Patients with Clostridioides difficile Infection and Cirrhosis – Yao-WenCheng – CLinial Gastroenterology and Hepatology

Association of Gut Microbiota-Dependent Metabolite Trimethylamine N-Oxide with First Ischemic Stroke – Taoping Sun – Journal of Atherosclerosis and Thrombosis

Dietary Strategies for Maintenance of Clinical Remission in Inflammatory Bowel Diseases: Are We There Yet? – Konstantinos Gkikas – Nutrients

The duodenal microbiome is altered in small intestinal bacterial overgrowth – Gabriela Leite – PlosOne

Faecal microbiota transplantation: A life-saving therapy challenged by commercial claims for exclusivity – Christian LodbergHvas – EClinical Medicine

Animal experiments

Microbiota modulate sympathetic neurons via a gut–brain circuit – Paul A. Muller – Nature

Prototypical pacemaker neurons interact with the resident microbiota – Alexander Klimovich – PNAS

Gut microbiota dysbiosis and altered tryptophan catabolism contribute to autoimmunity in lupus-susceptible mice – Seung-Chul Choi – Science Translational Medicine

The relationship between gut microbiota and short chain fatty acids in the renal calcium oxalate stones disease – Yu Liu – Faseb Journal

Sodium Butyrate Alleviates Mouse Colitis by Regulating Gut Microbiota Dysbiosis – Xiujing Dou – Animals

Dietary sphinganine is selectively assimilated by members of the mammalian gut microbiome – Min-Ting Lee – Journal of Lipid Research

Commentary: Modulating microbiome metabolites in vivo – Chun-Jun Guo – Science

Plant, root and soil microbiome

Quantitative comparison between the rhizosphere effect of Arabidopsis thaliana and co-occurring plant species with a longer life history – Martinus Schneijderberg – ISME Journal

Water microbiome

Anthropogenic dissolved organic carbon and marine microbiomes – Maria Vila-Costa – ISME Journal

Functional foods

Effect of a functional fibre supplement on glycemic control when added to a year-long medically supervised weight management program in adults with type 2 diabetes – Raylene A. Reimer – European Journal of Clinical Nutrition

Prenatal exposure to the probiotic Lactococcus lactis decreases anxiety-like behavior and modulates cortical cytoarchitecture in a sex specific manner – Natalia Surzenko – PlosOne

Non microbiology picks

SARS-CoV-2 is transmitted via contact and via the air between ferrets – Mathilde Richard – Nature Communications

June 3, 2020

Today’s post covers articles on role of microbiome in sepsis, early life microbiota related to cystic fibrosis and respiratory syncitial virus disease, promise and challenge with cancer microbiome, effect of probiotics on intestinal homeostasis after chemotherapy and many more!

General microbiome

Predictive biology: modelling, understanding and harnessing microbial complexity – Allison J. Lopatkin – Nature Reviews Microbiology

The Gut Microbiome’s Role in the Development, Maintenance, and Outcomes of Sepsis – Max W Adelman – Critical Care

The Promise and Challenge of Cancer Microbiome Research – Sumeed Syed Manzoor – Genome Biology

Antidiabetic Effects of Flavan-3-ols and Their Microbial Metabolites – Estefanía Márquez Campos – Nutrients

Human microbiome

Longitudinal analysis reveals transition barriers between dominant ecological states in the gut microbiome – Roie Levy – PNAS

Strain-resolved microbiome sequencing reveals mobile elements that drive bacterial competition on a clinical timescale – Soumaya Zlitni – Genome Medicine

Comparative Assessment of Faecal Microbial Composition and Metabonome of Swine, Farmers and Human Control – Shiang Chiet Tan – Scientific Reports

Matching Between Donors and Ulcerative Colitis Patients Is Important for Long-Term Maintenance After Fecal Microbiota Transplantation – Koki Okahara – Journal of Clinical Medicine

Preganancy and early life

Alterations in Vaginal Microbiota and Associated Metabolome in Women With Recurrent Implantation Failure – Min Fu – mBio

Development of the Gut Microbiota in Early Life: The Impact of Cystic Fibrosis and Antibiotic Treatment – Maartje Kristensen – Journal of Cystic Fibrosis

Altered Gut Microbiota in Infants Is Associated With Respiratory Syncytial Virus Disease Severity – Jeffrey N Harding – BMC Microbiology

Ecological Succession in the Vaginal Microbiota During Pregnancy and Birth – M A Rasmussen – Isme Journal

Animal experiments

Host genotype and exercise exhibit species-level selection for members of the gut bacterial communities in the mouse digestive system – R. A. Dowden – Scientific Reports

Repetitive, Mild Traumatic Brain Injury Results in a Progressive White Matter Pathology, Cognitive Deterioration, and a Transient Gut Microbiota Dysbiosis – Mariana Angoa-Pérez – Scientific Reports

Association of Gut Microbiota Composition and Function With an Aged Rat Model of Senile Osteoporosis Using 16S rRNA and Metagenomic Sequencing Analysis – Sicong Ma – Aging

Increasing the Hindgut Carbohydrate/Protein Ratio by Cecal Infusion of Corn Starch or Casein Hydrolysate Drives Gut Microbiota-Related Bile Acid Metabolism To Stimulate Colonic Barrier Function – Yu Pi – mSystems

Plant, root and soil microbiome

Using Soil Bacterial Communities to Predict Physico-Chemical Variables and Soil Quality – Syrie M Hermans – Microbiome

Analysis of bacterial and archaeal communities associated with Fogo volcanic soils of different ages – Corinne Biderre-Petit – Fems Microbial Ecology

Water microbiome

Functional potential and assembly of microbes from sediments in a lake bay and adjoining river ecosystem for polycyclic aromatic hydrocarbon biodegradation – Zaisheng Yan – Environmental Microbiology

Functional foods

Effect of Probiotics on the Maintenance of Intestinal Homeostasis After Chemotherapy: Systematic Review and Meta-Analysis of Pre-Clinical Studies – W G Lima – Beneficial Microbes

Non microbiology picks

Racial Disparities in Knowledge, Attitudes and Practices Related to COVID-19 in the USA– Wilson M Alobuia – Journal of Public Health

Ozone Treatment for Elimination of Bacteria and SARS-CoV-2 for Medical Environments – Craig Westover – BioRxiv

Probiotics to precision probiotics

After “precision medicine”, it is now time to conceptualize the term “precision probiotics”. In simple words, fundamental idea of precision medicine is to develop “new taxonomy” of disease employing molecular characterization of disease based on individual data that will enable better stratification of patients and determining most effective treatments. On similar lines, Veiga and colleagues offer strategies to develop precision probiotics, combine with multi-omics host response data to find most optimal probiotic modality in stratified individuals/populations.

I would recommend to read the review in full. To motivate you, following are some excerpts from the review:

“Historically, the discovery of probiotics relied on a top-down approach, where a microorganism enriched in healthy individuals (compared to an altered health state) is suggested to be beneficial and correlates with a health benefit upon administration to humans…While this empirical top-down approach provides robust leads for the development of probiotics, in the absence of prior mechanistic information, it inherently necessitates multiple cycles of trial and error to identify health benefits.”

Problems with top-down approach

  • “Probiotic efficacy being both strain- and indication-specific
  • Person-specific factors also contribute to heterogeneity in the outcome of probiotic supplementations, including diet, age and the microbiome. Colonization-resistant microbiomes are more resilient to probiotic interventions compared to colonization-permissive individuals.”

Bottom up approach

“The phenotypic approach is based on screening for probiotic effects using in vitro and ex vivo cell cultures as well as animal models with immune, neuronal, metabolic or microbial read-outs.

Target-based discovery relies on the selection of probiotic candidates based primarily on in silico prediction of their capacity to produce molecular effectors that are potentially able to modulate host or microbial pathways, which are foreseen to play a critical role in health or disease. Such in silico predictions would require the use of multi-omics (such as genomics, transcriptomics, metabolomics and proteomics) possibly coupled to metabolic reconstruction to infer the metabolic capacity of the screened microorganisms.”

Challenges with bottom-up approach

  • “A greater challenge lies in applying a person-specific approach to predict efficacy, which likely requires obtaining profound individualized host data (including genetics, anthropometrics and immune profiling) and microbiome data (such as strain-level composition, transcriptomics and metabolomics), as well as identifying relevant biomarkers that predict colonization resistance and/or a health outcome.
  • As stool samples do not accurately reflect colonization and impact on the gut microbiota along the gastrointestinal tract during probiotic supplementation, there is a great need to devise non-invasive means for identifying compatible probiotic–individual matches.
  • Another important factor to consider is safety, as exogenous microorganisms can have unexpected effects on the microbiome, and can even compromise the health of vulnerable subjects and result in bacteraemia or fungaemia.”

I believe that these challenges also hold true for top-down approach

Precision probiotics strategies

The big aim

“…developing algorithms that, when provided with these individualized parameters, can suggest the optimal probiotic modality that would result in a beneficial outcome.”

  • “To achieve this goal, on one hand, scientists need to better characterize the physiological or pathological pathways that can be modulated by probiotics, in line with the increasing effort to use bottom-up approaches.
  • On the other hand, further digitization of tools for the collection and processing of person-specific data, and their integration with genomic and metabolomic host and microbiome profiles, will be required.
  • Setting up standardized protocols that allow bio-citizens to self-experiment in ‘N-of-1 trials’ and report their experiences with probiotics, coupled with individualized measurements, would greatly expand our understanding of differential probiotic activity in the heterogenous human population. This approach will require devising strict validation and safety measurements for promising centralized data collection while maintaining participants’ anonymity.

“…While today, this (refers to microbiome data) personal information is poorly actionable, tomorrow it could serve as the basis for microbiome-centred precision nutrition and preventive medicine, including precision probiotics.”

April 5, 2020.

All the break-neck speed with which the progress that is happening today in tracking, detecting and treating the disease, like everything else, is owed in part to the giants whose shoulders we’re standing on. One such thing is the usage of serum (from recovered patients or derived elsewhere) for treatment. So, as a little tribute, I would like to share with you today, on the birthday of Dr. Hattie Elizabeth Alexander (born April 5, 1901), the information that she pioneered the work in using anti-influenzal rabbit serums to treat the then always-fatal influenzal meningitis (effectively bringing down the fatality rate to 20%!), and was also sone of the very first to study bacterial mutations that come along with antibiotic resistance !

So we’ve come a long way and are forging our way forward. Here are a few interesting articles that are slowly pushing this boundary, a piece at a time.

COVID-19

From PREDICT to prevention, one pandemic later – Colin J Carlson – The Lancet.

Human Microbiome

Review: Risk factors associated with gastric malignancy during chronic Helicobacter pylori infection – Ami Y Seegar – Medical Research Archives.

Review: From Association to Causality: the Role of the Gut Microbiota and Its Functional Products on Host Metabolism – Ara Koh – Molecular Cell.

Pregnancy and Early Life

Breast Milk and Microbiota in the Premature Gut: A Method of Preventing Necrotizing Enterocolitis – Orga PL et al – Karger.

Human Brain and Microbiome

Book: Integrative and Functional Medical Nutrition Therapy. Chapter: The Microbiome and Brain Health – Sharon L. Norling -Springer

Animal Experiments


Integrated omics profiling of dextran sodium sulfate-induced colitic mice supplemented with Wolfberry (Lycium barbarum). Wanping Aw et al – NPJ Science of Food.

Botany

Rhizobacteriome: Promising Candidate for Conferring Drought Tolerance in Crops – Vinod Yadav et al – Journal of Pure Applied Microbiology

Legionella species: A potential problem associated with rain water harvesting systems? – Judith A Taylor et al – SAGE Journals

Bioinformatics

Applications of Machine Learning Predictive Models in the Chronic Disease Diagnosis – Gopi Battineni et al – Journal of Personalized Medicine

PS: I know, I am with you on this — the lockdown isn’t ideal. But we are also the generation, who for the first time can end articles signing off as “Stay Safe and Wash Your Hands” and manage to prevent a large proportion of its species from suffering / dying. Isn’t that crazy! Have a great day!

More information on Dr. Hattie Elizabeth Alexander — here and here.

January 27, 2020

In today’s Monday morning post – establishing causality for gut microbiome using human microbiota associated rodents, gut microbiota profiling in pregnant women after bariatric surgery, proteomics changes in bacteria, discovery of core microbiome of common bean rhizosphere and many more.

General Microbiome

Establishing or Exaggerating Causality for the Gut Microbiome: Lessons from Human Microbiota-Associated Rodents – Jens Walter – Cell

Microbial Genomics and Metagenomics in India: Explorations and Perspectives– Princy Hira – Proceedings of Indian National Science Academy

Human Microbiome

Longitudinal metabolic and gut bacterial profiling of pregnant women with previous bariatric surgery – Kiana Ashley West – Gut

Identifying determinants of bacterial fitness in a model of human gut microbial succession – Lihui Feng – PNAS

16S rDNA microbiome composition pattern analysis as a diagnostic biomarker for biliary tract cancer – Huisong Lee – World Journal of Surgical Oncology

Faecal microbiota transplantations and urinary tract infections – Jean Christophe Lagier – Lancet

Animal Microbiome

Influences of a Prolific Gut Fungus (Zancudomyces culisetae) on Larval and Adult Mosquito (Aedes aegypti)-Associated Microbiota – Jonas Frankel-Bricker – Applied and Environmental Microbiology

Functional dynamics of bacterial species in the mouse gut microbiome revealed by metagenomic and metatranscriptomic analyses – Youn Wook Chung – PlosOne

Early life microbiome perturbation alters pulmonary responses to ozone in male mice – Traci A. Brown – Physiological Reports

Evolution and maintenance of microbe-mediated protection under occasional pathogen attack – Anke Kloock – BioRxiv

Plant, root and soil microbiome

Community sequencing on a natural experiment reveals little influence of host species and timing but a strong influence of compartment on the composition of root endophytes in three annual Brassicaceae – Jose G Macia-Vicente – BioRxiv

Discovery of a spatially and temporally persistent core microbiome of the common bean rhizosphere – Nejc Stopnisek – BioRxiv

Resident and phytometer plants host comparable rhizosphere fungal communities in managed grassland ecosystems – Ricardo Schöps – Scientific Reports

Evaluation of fatty acid derivatives in the remediation of aged PAH-contaminated soil and microbial community and degradation gene response – Qingling Wang – Chemosphere

Techniques

Proteomic changes in bacteria caused by exposure to environmental conditions can be detected by Matrix-Assisted Laser Desorption/Ionization – Time of Flight (MALDI-ToF) Mass Spectrometry – Denise Chac – BioRxiv

Probiotics, prebiotics

Beneficial bile acid metabolism from Lactobacillus plantarum of food origin – Roberta Prete – Scientific Reports

Microbes in the news

Could a kid’s microbiome alter their behaviour? – Health24

Microbiome Therapeutics Market Report Forecast by Capital Investment, Industry Outlook, Opportunities & Trends 2024 – Fusion Science Academy

November 11, 2019

Monday’s morning digest is all about interesting updates in microbiome field – real time sampling of international travelers to study antibiotic resistant bacteria, new techniques on using rectal swabs instead of fecal samples to study infant microbiota, 16srRNA gene sequencing for strain level identification and if neutraceutical consumption helps in multiple sclerosis! Finally some interesting review articles on microbial ecology in wine making and a Movember month featured article on association of gut microbiome with men’s sexual health. Enjoy reading!

General microbiome

From the vineyard to the winery: how microbial ecology drives regional distinctiveness of wine – Di Liu – Frontiers in Microbiology

The Gut Microbiome and Men’s Sexual Health – Mohamad M. Osman – Current Sexual Heath Reports

Antibacterial Soaps and Other Cleaners May Actually Be Aiding in the Development of Super Bacteria – Shimon Shatzmiller – Pharmacology, Toxicology and Pharmaceutics

Dietary lipids, gut microbiota and lipid metabolism – Marc Schoeler – Reviews in Endocrine and Metabolic Disorders

Human microbiome

Functional characterisation of gut microbiota and metabolism in Type 2 diabetes indicates that Clostridiales and Enterococcus could play a key role in the disease – Marina Mora-Ortiz – BioRxiv

Real-time sampling of travelers shows intestinal colonization by multidrug-resistant bacteria to be a dynamic process with multiple transient acquisitions – A. Kantele – BioRxiv

A multi-omic cohort as a reference point for promoting a healthy human gut microbiome – Zhuye Jie – BioRxiv

Antimicrobial resistance gene prevalence in a population of patients with advanced dementia is related to specific pathobionts – Aislinn D. Rowan-Nash – BioRxiv

Genomic characterization of the non-O1/non-O139 Vibrio cholerae strain that caused a gastroenteritis outbreak in Santiago, Chile, 2018 – Mónica Arteaga – BioRxiv

Molecular Reconstruction of the Diet in Human Stool Samples – Frank Maixner – mSystems

Infant microbiome

Impacts of Delivery Mode on Very Low Birth Weight Infants’ Oral Microbiome – Hongping Li – Pediatrics and Neonatology

Biomarker Research in ADHD: the Impact of Nutrition (BRAIN) – study protocol of an open-label trial to investigate the mechanisms underlying the effects of a few-foods diet on ADHD symptoms in children – Tim Stobernack – BMJ Open

Immunometabolic approaches to prevent, detect, and treat neonatal sepsis – Maria Giulia Conti – Pediatric Research

Rectal swabs are a reliable proxy for faecal samples in infant gut microbiota research based on 16S-rRNA sequencing – Marta Reyman – Scientific Reports

Gut microbiome of treatment-naïve MS patients of different ethnicities early in disease course – R. E. Ventura – Scientific Reports

Animal experiments

Vasoactive intestinal peptide deficiency is associated with altered gut microbiota communities in male and female C57BL/6 mice – Manpreet Bains – Frontiers in Microbiology

Metabolic analysis of regionally distinct gut microbial communities using an in vitro platform – Jenni Firrman – Agricultural and Environmental Chemistry

Effect of Diet on the Enteric Microbiome of the Wood-Eating Catfish Panaque nigrolineatus – Harold J. Schreier – Frontiers in Microbiology

A high-fat/high-protein, Atkins-type diet exacerbates Clostridioides (Clostridium) difficile infection in mice, whereas a high-carbohydrate diet protects – Chrisabelle C. Mefferd – BioRxiv

Plant, soil, root microbiome

Effects of repeated applications of urea with DMPP on ammonia oxidizers, denitrifiers, and non-targeted microbial communities of an agricultural soil in Queensland, Australia – Aineah Obed Luchibia – Applied Soil Ecology

Covariation of diet and gut microbiome in African megafauna – Tyler R. Kartzinel – PNAS

Fungal communities resist recovery in sand mine restoration – Miranda Hart – Frontiers in Forest and Global Change

Microbial community structure and ecology in sediments of a pristine mangrove forest – C.O.Santana – BioRxiv

Bridging the gap between single-strain and community-level plant-microbe chemical interactions – Bridget O’Banion – Molecular Plant-Microbe Interactions

A brief from the leaf: latest research to inform our understanding of the phyllosphere microbiome – Johan HJ Leveau – Current Opinion in Microbiology

Water microbiome

Metabolic and biogeochemical consequences of viral infection in aquatic ecosystems Amy E. Zimmerman – Nature Reviews Microbiology

Down to the bone: the role of overlooked endolithic microbiomes in reef coral health – Mathieu Pernice – ISME Journal

Differential responses of stream water and bed sediment microbial communities to watershed degradation – Hehuan Liao – Environment International

B12 production by marine microbial communities and Dinoroseobacter shibae continuous cultures under different growth and respiration rates – Josue Villegas-Mendoza – Aquatic Microbial Ecology

Quantifying the contribution of microbial immigration in engineered water systems – Ran Mei – Microbiome

Microbial community rearrangements in power-to-biomethane reactors employing mesophilic biogas digestate – Norbert Ács – Frontiers in Energy Research

Techniques

Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis – Jethro S. Johnson – Nature Communications

AMR – An R Package for Working with Antimicrobial Resistance Data – Matthijs S. Berends – BioRxiv

Probiotics Prebiotics

The effect of emerging nutraceutical interventions for clinical and biological outcomes in multiple sclerosis: A systematic review – Wolfgang Marx – Multiple Sclerosis and Related Disorders

Resveratrol treatment improves the altered metabolism and related dysbiosis of gut programed by prenatal high-fat diet and postnatal high-fat diet exposure – Yi-Chuan Huang – The Journal of Nutritional Biochemistry

The effects of inulin on gut microbial composition: a systematic review of evidence from human studies – Quentin Le Bastard – European Journal of Clinical Microbiology & Infectious Diseases

November 8, 2019

Today’s week-end digest is about new bioinformatic tools (MGnify, PIME, MDiNE) for microbiota analysis, how chemical and built environment of home affects human microbiota and  guidelines for the gut microbiome studies in hypertension.

General microbiome

Adaptation of the Gut Microbiota to Modern Dietary Sugars and Sweeteners – Sara C. Di Rienzi – Advances in Nutrition

Bacteriophages in gastroenterology—from biology to clinical applications – João Sabino – Alimentary Pharmacology and Therapeutics

Boosting natural history research via metagenomic clean-up of crowdsourced feces – Amrita Srivathsan – Plos Biology

Human microbiome

Lower gut microbiome diversity and higher abundance of proinflammatory genus Collinsella are associated with biopsy-proven nonalcoholic steatohepatitis – Stuart Astbury – Gut Microbes

Guidelines for Transparency on Gut Microbiome Studies in Essential and Experimental Hypertension – Francine Z. Marques – Hypertension

The association between dietary fibre deficiency and high-income lifestyle-associated diseases: Burkitt’s hypothesis revisited – Stephen J. O’Keefe – The Lancet Gastroenterology and Hepatology

Animal experiments

Bacterial Swarming as a Protective Response to Intestinal Stress – Weijie Chen – BioRxiv

Flaxseed oil supplementation improves intestinal function and immunity, associated with altered intestinal microbiome and fatty acid profile in pigs with intrauterine growth retardation – Lianqiang Che – Food and Function

Gamma-aminobutyric acid-producing lactobacilli positively affect metabolism and depressive-like behaviour in a mouse model of metabolic syndrome – E. Patterson – Scientific Reports

Plant, root and soil microbiome

Short term effects of different green manure amendments on the composition of main microbial groups and microbial activity of a submerged rice cropping system – Muhammad Israr Khan – Applied Soil Ecology

Cost-effective in-situ remediation technologies for complete mineralization of dyes contaminated soils – Vipul R. Patel – Chemosphere

Distinct Microbial Community of Phyllosphere Associated with Five Tropical Plants on Yongxing Island, South China Sea – Lijun Bao – Microorganisms

Tracing the evolutionary routes of plant–microbiota interactions – Carmen Escudero-Martinez – Current Opinion in Microbiology

Water microbiome

Diet shapes cold‐water corals bacterial communities – Pierre E. Galand – Environmental Microbiology

Built Environment

Home chemical and microbial transitions across urbanization – Laura-Isobel McCall – Nature Microbiology

Techniques

Learning representations of microbe–metabolite interactions – James T. Morton – Nature Methods

MGnify: the microbiome analysis resource in 2020 – Alex L. Mitchell – Nucleic Acids Research

PIME: A package for discovery of novel differences among microbial communities – Luiz Fernando W. Roesch – Molecular Ecology Resources

MDiNE: A model to estimate differential co-occurrence networks in microbiome studies – Kevin McGregor – Bioinformatics

Probiotics

Fermentation of plant-based milk alternatives for improved flavour and nutritional value – Muzi Tangyu – Applied Microbiology and Biotechnology

Modulations of Probiotics on Gut Microbiota in a 5‐Fluorouracil‐Induced Mouse Model of Mucositis – Chun Yan Yeung – Journal of Gastroenterology and Hepatology

The effect of an additive containing three Lactobacillus species on the fermentation pattern and microbiological status of silage – Maja Fijałkowska – Journal of the Science of Food and Agriculture

Microbes in the news

Gut Microbiome Puts the Brakes on Iron Absorption – Michigan Medicine

The Link Between Sleep and Your Gut Microbiome – Health central

Microbiome in China: Cosmetic trend will ‘heat up’ by the end of 2020, says expert – Cosmetics Design-Asia

Enterome Enters Research Collaboration With Major Cancer Center Focused on New Microbiome-derived Immunotherapies – Yahoo Finance

Non Microbiology Picks

Is running associated with a lower risk of all-cause, cardiovascular and cancer mortality, and is the more the better? A systematic review and meta-analysis – Zeljko Pedisic – British Journal of Sports Medicine